Hi there,
Normally travelling during the daytime (eg, not on a sleeper) is a very straightforwards journey, and as it's exclusively on JR lines and trains will incur no extra charges. Here is a sample itinerary for you.
In the past, before the final link in the Tohoku Shinkansen line between Hachinohe and Shin-Aomori was built, you had to change train at Hachinohe to the non-JR line ran by Aoimori Railways (this was still free for jrpass holders). Nowadays, with the completion of the Tohoku shinkansen, you can travel all the way up to Shin-Aomori in one hop from Tokyo. In fact, on the Japan Rail Pass validity site you can still see the remnants of this rule which lets you travel between Hachinohe and Shin-Aomori on the (slower) Aoimori Railways lines for free as long as you do not disembark.
The simple answer is there are no extra fees from Tokyo-Sapporo for Japan Rail Pass holders.
If you have an itinerary detailed, I'd be happy to review it.
Hope this helps!